I also have a Hiace and went through something similar only last week!
Your van batteries should be wired in parallel, so there should be a thick cable from the +ve on one to the +ve on the other. Ditto for the -ve. Thanks to this, even if you're wired to one of the batteries, you're working off both.
Number one - make sure that all connections are tight. That was my problem, but we'd already gone through the rest before finding that out. Donkeys.
Test number two, start the engine and put your voltmeter from +ve (either) to -ve (ditto). Should read in excess of 13V. If below, you have an alternator problem. If not carry on.
To check whether one battery is knackered without resetting everything like radio, alarm, etc, what you need to do is to disconnect one end of one of the cables that runs between the negative terminals (doesn't matter which).
Then put a voltmeter across each battery in turn. They should be above about 12.5V as an absolute minimum, ideally closer to 13V. If one or other seriously underreads 12.5V, that battery may well be cream crackered.
If they are all OK then you're probably looking at getting an auto electrician to look at it. If you go to a garage they'll get an electrician to look at it and charge you margin on top.
Also, loads of decent batteries these days come with three year guarantees, so check before you buy a new one that it isn't covered.
Good luck,
Vin